# | Line 12 | Line 12 | |
---|---|---|
12 | #include "mpiSimulation.hpp" | |
13 | #endif | |
14 | ||
15 | + | // some defines for ensemble and Forcefield cases |
16 | + | |
17 | + | #define NVE_ENS 0 |
18 | + | #define NVT_ENS 1 |
19 | + | #define NPT_ENS 2 |
20 | + | |
21 | + | #define FF_DUFF 0 |
22 | + | #define FF_LJ 1 |
23 | + | |
24 | + | |
25 | SimSetup::SimSetup(){ | |
26 | stamps = new MakeStamps(); | |
27 | globals = new Globals(); | |
# | Line 66 | Line 76 | void SimSetup::createSim( void ){ | |
76 | ||
77 | MakeStamps *the_stamps; | |
78 | Globals* the_globals; | |
79 | < | int i, j; |
79 | > | int i, j, k, globalAtomIndex; |
80 | > | |
81 | > | int ensembleCase; |
82 | > | int ffCase; |
83 | > | |
84 | > | ensembleCase = -1; |
85 | > | ffCase = -1; |
86 | ||
87 | // get the stamps and globals; | |
88 | the_stamps = stamps; | |
# | Line 80 | Line 96 | void SimSetup::createSim( void ){ | |
96 | // get the ones we know are there, yet still may need some work. | |
97 | n_components = the_globals->getNComponents(); | |
98 | strcpy( force_field, the_globals->getForceField() ); | |
99 | + | |
100 | + | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
101 | + | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
102 | + | else{ |
103 | + | sprintf( painCave.errMsg, |
104 | + | "SimSetup Error. Unrecognized force field -> %s\n", |
105 | + | force_field ); |
106 | + | painCave.isFatal = 1; |
107 | + | simError(); |
108 | + | } |
109 | + | |
110 | + | // get the ensemble: |
111 | strcpy( ensemble, the_globals->getEnsemble() ); | |
112 | + | |
113 | + | if( !strcasecmp( ensemble, "NVE" )) ffCase = NVE_ENS; |
114 | + | else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS; |
115 | + | else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS; |
116 | + | else{ |
117 | + | sprintf( painCave.errMsg, |
118 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
119 | + | "reverting to NVE for this simulation.\n", |
120 | + | ensemble ); |
121 | + | painCave.isFatal = 0; |
122 | + | simError(); |
123 | + | strcpy( ensemble, "NVE" ); |
124 | + | ensembleCase = NVE_ENS; |
125 | + | } |
126 | strcpy( simnfo->ensemble, ensemble ); | |
127 | + | |
128 | + | |
129 | + | // if( !strcasecmp( ensemble, "NPT" ) ) { |
130 | + | // the_extendedsystem = new ExtendedSystem( simnfo ); |
131 | + | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
132 | + | // if (the_globals->haveTargetPressure()) |
133 | + | // the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
134 | + | // else { |
135 | + | // sprintf( painCave.errMsg, |
136 | + | // "SimSetup error: If you use the constant pressure\n" |
137 | + | // " ensemble, you must set targetPressure.\n" |
138 | + | // " This was found in the BASS file.\n"); |
139 | + | // painCave.isFatal = 1; |
140 | + | // simError(); |
141 | + | // } |
142 | + | |
143 | + | // if (the_globals->haveTauThermostat()) |
144 | + | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
145 | + | // else if (the_globals->haveQmass()) |
146 | + | // the_extendedsystem->setQmass(the_globals->getQmass()); |
147 | + | // else { |
148 | + | // sprintf( painCave.errMsg, |
149 | + | // "SimSetup error: If you use one of the constant temperature\n" |
150 | + | // " ensembles, you must set either tauThermostat or qMass.\n" |
151 | + | // " Neither of these was found in the BASS file.\n"); |
152 | + | // painCave.isFatal = 1; |
153 | + | // simError(); |
154 | + | // } |
155 | ||
156 | + | // if (the_globals->haveTauBarostat()) |
157 | + | // the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
158 | + | // else { |
159 | + | // sprintf( painCave.errMsg, |
160 | + | // "SimSetup error: If you use the constant pressure\n" |
161 | + | // " ensemble, you must set tauBarostat.\n" |
162 | + | // " This was found in the BASS file.\n"); |
163 | + | // painCave.isFatal = 1; |
164 | + | // simError(); |
165 | + | // } |
166 | + | |
167 | + | // } else if ( !strcasecmp( ensemble, "NVT") ) { |
168 | + | // the_extendedsystem = new ExtendedSystem( simnfo ); |
169 | + | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
170 | + | |
171 | + | // if (the_globals->haveTauThermostat()) |
172 | + | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
173 | + | // else if (the_globals->haveQmass()) |
174 | + | // the_extendedsystem->setQmass(the_globals->getQmass()); |
175 | + | // else { |
176 | + | // sprintf( painCave.errMsg, |
177 | + | // "SimSetup error: If you use one of the constant temperature\n" |
178 | + | // " ensembles, you must set either tauThermostat or qMass.\n" |
179 | + | // " Neither of these was found in the BASS file.\n"); |
180 | + | // painCave.isFatal = 1; |
181 | + | // simError(); |
182 | + | // } |
183 | + | |
184 | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); | |
185 | simnfo->usePBC = the_globals->getPBC(); | |
186 | ||
187 | + | int usesDipoles = 0; |
188 | + | switch( ffCase ){ |
189 | ||
190 | + | case FF_DUFF: |
191 | + | the_ff = new DUFF(); |
192 | + | usesDipoles = 1; |
193 | + | break; |
194 | ||
195 | < | if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
196 | < | else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
197 | < | else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
198 | < | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
199 | < | else{ |
195 | > | case FF_LJ: |
196 | > | the_ff = LJFF(); |
197 | > | break; |
198 | > | |
199 | > | default: |
200 | sprintf( painCave.errMsg, | |
201 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
98 | < | force_field ); |
201 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
202 | painCave.isFatal = 1; | |
203 | simError(); | |
204 | } | |
# | Line 105 | Line 208 | void SimSetup::createSim( void ){ | |
208 | MPIcheckPoint(); | |
209 | #endif // is_mpi | |
210 | ||
108 | – | |
109 | – | |
211 | // get the components and calculate the tot_nMol and indvidual n_mol | |
212 | the_components = the_globals->getComponents(); | |
213 | components_nmol = new int[n_components]; | |
# | Line 230 | Line 331 | void SimSetup::createSim( void ){ | |
331 | simnfo->n_torsions = tot_torsions; | |
332 | simnfo->n_SRI = tot_SRI; | |
333 | simnfo->n_mol = tot_nmol; | |
233 | – | |
334 | ||
335 | + | simnfo->molMembershipArray = new int[tot_atoms]; |
336 | + | |
337 | #ifdef IS_MPI | |
338 | ||
339 | // divide the molecules among processors here. | |
340 | ||
341 | mpiSim = new mpiSimulation( simnfo ); | |
342 | ||
241 | – | |
242 | – | |
343 | globalIndex = mpiSim->divideLabor(); | |
344 | ||
245 | – | |
246 | – | |
345 | // set up the local variables | |
346 | ||
347 | int localMol, allMol; | |
348 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
349 | + | |
350 | + | int* mol2proc = mpiSim->getMolToProcMap(); |
351 | + | int* molCompType = mpiSim->getMolComponentType(); |
352 | ||
353 | allMol = 0; | |
354 | localMol = 0; | |
# | Line 255 | Line 356 | void SimSetup::createSim( void ){ | |
356 | local_bonds = 0; | |
357 | local_bends = 0; | |
358 | local_torsions = 0; | |
359 | + | globalAtomIndex = 0; |
360 | + | |
361 | + | |
362 | for( i=0; i<n_components; i++ ){ | |
363 | ||
364 | for( j=0; j<components_nmol[i]; j++ ){ | |
365 | ||
366 | < | if( mpiSim->getMyMolStart() <= allMol && |
263 | < | allMol <= mpiSim->getMyMolEnd() ){ |
366 | > | if( mol2proc[allMol] == worldRank ){ |
367 | ||
368 | local_atoms += comp_stamps[i]->getNAtoms(); | |
369 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 268 | Line 371 | void SimSetup::createSim( void ){ | |
371 | local_torsions += comp_stamps[i]->getNTorsions(); | |
372 | localMol++; | |
373 | } | |
374 | < | allMol++; |
374 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
375 | > | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
376 | > | globalAtomIndex++; |
377 | > | } |
378 | > | |
379 | > | allMol++; |
380 | } | |
381 | } | |
382 | local_SRI = local_bonds + local_bends + local_torsions; | |
383 | ||
276 | – | |
384 | simnfo->n_atoms = mpiSim->getMyNlocal(); | |
385 | ||
386 | if( local_atoms != simnfo->n_atoms ){ | |
387 | sprintf( painCave.errMsg, | |
388 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
389 | < | " localAtom (%d) are note equal.\n", |
389 | > | " localAtom (%d) are not equal.\n", |
390 | simnfo->n_atoms, | |
391 | local_atoms ); | |
392 | painCave.isFatal = 1; | |
# | Line 304 | Line 411 | void SimSetup::createSim( void ){ | |
411 | Atom::createArrays(simnfo->n_atoms); | |
412 | the_atoms = new Atom*[simnfo->n_atoms]; | |
413 | the_molecules = new Molecule[simnfo->n_mol]; | |
414 | + | int molIndex; |
415 | ||
416 | + | // initialize the molecule's stampID's |
417 | ||
418 | + | #ifdef IS_MPI |
419 | + | |
420 | + | |
421 | + | molIndex = 0; |
422 | + | for(i=0; i<mpiSim->getTotNmol(); i++){ |
423 | + | |
424 | + | if(mol2proc[i] == worldRank ){ |
425 | + | the_molecules[molIndex].setStampID( molCompType[i] ); |
426 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
427 | + | the_molecules[molIndex].setGlobalIndex( i ); |
428 | + | molIndex++; |
429 | + | } |
430 | + | } |
431 | + | |
432 | + | #else // is_mpi |
433 | + | |
434 | + | molIndex = 0; |
435 | + | globalAtomIndex = 0; |
436 | + | for(i=0; i<n_components; i++){ |
437 | + | for(j=0; j<components_nmol[i]; j++ ){ |
438 | + | the_molecules[molIndex].setStampID( i ); |
439 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
440 | + | the_molecules[molIndex].setGlobalIndex( molIndex ); |
441 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
442 | + | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
443 | + | globalAtomIndex++; |
444 | + | } |
445 | + | molIndex++; |
446 | + | } |
447 | + | } |
448 | + | |
449 | + | |
450 | + | #endif // is_mpi |
451 | + | |
452 | + | |
453 | if( simnfo->n_SRI ){ | |
454 | < | the_sris = new SRI*[simnfo->n_SRI]; |
455 | < | the_excludes = new int[2 * simnfo->n_SRI]; |
454 | > | |
455 | > | Exclude::createArray(simnfo->n_SRI); |
456 | > | the_excludes = new Exclude*[simnfo->n_SRI]; |
457 | > | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
458 | simnfo->globalExcludes = new int; | |
459 | < | simnfo->n_exclude = tot_SRI; |
459 | > | simnfo->n_exclude = simnfo->n_SRI; |
460 | } | |
461 | else{ | |
462 | ||
463 | < | the_excludes = new int[2]; |
464 | < | the_excludes[0] = 0; |
465 | < | the_excludes[1] = 0; |
463 | > | Exclude::createArray( 1 ); |
464 | > | the_excludes = new Exclude*; |
465 | > | the_excludes[0] = new Exclude(0); |
466 | > | the_excludes[0]->setPair( 0,0 ); |
467 | simnfo->globalExcludes = new int; | |
468 | simnfo->globalExcludes[0] = 0; | |
469 | < | |
323 | < | simnfo->n_exclude = 1; |
469 | > | simnfo->n_exclude = 0; |
470 | } | |
471 | ||
472 | // set the arrays into the SimInfo object | |
473 | ||
474 | simnfo->atoms = the_atoms; | |
475 | < | simnfo->sr_interactions = the_sris; |
475 | > | simnfo->molecules = the_molecules; |
476 | simnfo->nGlobalExcludes = 0; | |
477 | simnfo->excludes = the_excludes; | |
478 | ||
479 | ||
480 | // get some of the tricky things that may still be in the globals | |
481 | ||
336 | – | if( simnfo->n_dipoles ){ |
337 | – | |
338 | – | if( !the_globals->haveRRF() ){ |
339 | – | sprintf( painCave.errMsg, |
340 | – | "SimSetup Error, system has dipoles, but no rRF was set.\n"); |
341 | – | painCave.isFatal = 1; |
342 | – | simError(); |
343 | – | } |
344 | – | if( !the_globals->haveDielectric() ){ |
345 | – | sprintf( painCave.errMsg, |
346 | – | "SimSetup Error, system has dipoles, but no" |
347 | – | " dielectric was set.\n" ); |
348 | – | painCave.isFatal = 1; |
349 | – | simError(); |
350 | – | } |
351 | – | |
352 | – | simnfo->rRF = the_globals->getRRF(); |
353 | – | simnfo->dielectric = the_globals->getDielectric(); |
354 | – | } |
355 | – | |
356 | – | #ifdef IS_MPI |
357 | – | strcpy( checkPointMsg, "rRf and dielectric check out" ); |
358 | – | MPIcheckPoint(); |
359 | – | #endif // is_mpi |
482 | ||
483 | if( the_globals->haveBox() ){ | |
484 | simnfo->box_x = the_globals->getBox(); | |
# | Line 407 | Line 529 | void SimSetup::createSim( void ){ | |
529 | ||
530 | the_ff->setSimInfo( simnfo ); | |
531 | ||
532 | < | makeAtoms(); |
532 | > | makeMolecules(); |
533 | simnfo->identArray = new int[simnfo->n_atoms]; | |
534 | for(i=0; i<simnfo->n_atoms; i++){ | |
535 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
414 | – | } |
415 | – | |
416 | – | if( tot_bonds ){ |
417 | – | makeBonds(); |
418 | – | } |
419 | – | |
420 | – | if( tot_bends ){ |
421 | – | makeBends(); |
422 | – | } |
423 | – | |
424 | – | if( tot_torsions ){ |
425 | – | makeTorsions(); |
536 | } | |
537 | + | |
538 | + | if (the_globals->getUseRF() ) { |
539 | + | simnfo->useReactionField = 1; |
540 | + | |
541 | + | if( !the_globals->haveECR() ){ |
542 | + | sprintf( painCave.errMsg, |
543 | + | "SimSetup Warning: using default value of 1/2 the smallest " |
544 | + | "box length for the electrostaticCutoffRadius.\n" |
545 | + | "I hope you have a very fast processor!\n"); |
546 | + | painCave.isFatal = 0; |
547 | + | simError(); |
548 | + | double smallest; |
549 | + | smallest = simnfo->box_x; |
550 | + | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
551 | + | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
552 | + | simnfo->ecr = 0.5 * smallest; |
553 | + | } else { |
554 | + | simnfo->ecr = the_globals->getECR(); |
555 | + | } |
556 | ||
557 | + | if( !the_globals->haveEST() ){ |
558 | + | sprintf( painCave.errMsg, |
559 | + | "SimSetup Warning: using default value of 0.05 * the " |
560 | + | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
561 | + | ); |
562 | + | painCave.isFatal = 0; |
563 | + | simError(); |
564 | + | simnfo->est = 0.05 * simnfo->ecr; |
565 | + | } else { |
566 | + | simnfo->est = the_globals->getEST(); |
567 | + | } |
568 | + | |
569 | + | if(!the_globals->haveDielectric() ){ |
570 | + | sprintf( painCave.errMsg, |
571 | + | "SimSetup Error: You are trying to use Reaction Field without" |
572 | + | "setting a dielectric constant!\n" |
573 | + | ); |
574 | + | painCave.isFatal = 1; |
575 | + | simError(); |
576 | + | } |
577 | + | simnfo->dielectric = the_globals->getDielectric(); |
578 | + | } else { |
579 | + | if (usesDipoles) { |
580 | + | |
581 | + | if( !the_globals->haveECR() ){ |
582 | + | sprintf( painCave.errMsg, |
583 | + | "SimSetup Warning: using default value of 1/2 the smallest " |
584 | + | "box length for the electrostaticCutoffRadius.\n" |
585 | + | "I hope you have a very fast processor!\n"); |
586 | + | painCave.isFatal = 0; |
587 | + | simError(); |
588 | + | double smallest; |
589 | + | smallest = simnfo->box_x; |
590 | + | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
591 | + | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
592 | + | simnfo->ecr = 0.5 * smallest; |
593 | + | } else { |
594 | + | simnfo->ecr = the_globals->getECR(); |
595 | + | } |
596 | + | |
597 | + | if( !the_globals->haveEST() ){ |
598 | + | sprintf( painCave.errMsg, |
599 | + | "SimSetup Warning: using default value of 5%% of the " |
600 | + | "electrostaticCutoffRadius for the " |
601 | + | "electrostaticSkinThickness\n" |
602 | + | ); |
603 | + | painCave.isFatal = 0; |
604 | + | simError(); |
605 | + | simnfo->est = 0.05 * simnfo->ecr; |
606 | + | } else { |
607 | + | simnfo->est = the_globals->getEST(); |
608 | + | } |
609 | + | } |
610 | + | } |
611 | ||
612 | + | #ifdef IS_MPI |
613 | + | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
614 | + | MPIcheckPoint(); |
615 | + | #endif // is_mpi |
616 | ||
430 | – | |
431 | – | |
432 | – | |
617 | if( the_globals->haveInitialConfig() ){ | |
618 | ||
619 | InitializeFromFile* fileInit; | |
# | Line 583 | Line 767 | void SimSetup::createSim( void ){ | |
767 | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); | |
768 | ||
769 | ||
770 | < | // // make the longe range forces and the integrator |
770 | > | // make the integrator |
771 | ||
772 | < | // new AllLong( simnfo ); |
772 | > | switch( ensembleCase ){ |
773 | ||
774 | < | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
775 | < | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
776 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
593 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
774 | > | case NVE_ENS: |
775 | > | new NVE( simnfo, the_ff ); |
776 | > | break; |
777 | ||
778 | + | default: |
779 | + | sprintf( painCave.errMsg, |
780 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
781 | + | painCave.isFatal = 1; |
782 | + | simError(); |
783 | + | } |
784 | ||
785 | ||
786 | + | #ifdef IS_MPI |
787 | + | mpiSim->mpiRefresh(); |
788 | + | #endif |
789 | + | |
790 | // initialize the Fortran | |
791 | < | |
791 | > | |
792 | > | |
793 | simnfo->refreshSim(); | |
794 | ||
795 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 620 | Line 814 | void SimSetup::createSim( void ){ | |
814 | #endif // is_mpi | |
815 | } | |
816 | ||
623 | – | void SimSetup::makeAtoms( void ){ |
817 | ||
818 | < | int i, j, k, index; |
626 | < | double ux, uy, uz, uSqr, u; |
627 | < | AtomStamp* current_atom; |
818 | > | void SimSetup::makeMolecules( void ){ |
819 | ||
820 | + | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
821 | + | molInit info; |
822 | DirectionalAtom* dAtom; | |
823 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
823 | > | LinkedAssign* extras; |
824 | > | LinkedAssign* current_extra; |
825 | > | AtomStamp* currentAtom; |
826 | > | BondStamp* currentBond; |
827 | > | BendStamp* currentBend; |
828 | > | TorsionStamp* currentTorsion; |
829 | ||
830 | < | lMolIndex = 0; |
831 | < | molIndex = 0; |
832 | < | index = 0; |
635 | < | for( i=0; i<n_components; i++ ){ |
830 | > | bond_pair* theBonds; |
831 | > | bend_set* theBends; |
832 | > | torsion_set* theTorsions; |
833 | ||
834 | < | for( j=0; j<components_nmol[i]; j++ ){ |
834 | > | |
835 | > | //init the forceField paramters |
836 | ||
837 | < | #ifdef IS_MPI |
640 | < | if( mpiSim->getMyMolStart() <= molIndex && |
641 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
642 | < | #endif // is_mpi |
837 | > | the_ff->readParams(); |
838 | ||
839 | < | molStart = index; |
840 | < | nMemb = comp_stamps[i]->getNAtoms(); |
646 | < | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
647 | < | |
648 | < | current_atom = comp_stamps[i]->getAtom( k ); |
649 | < | if( current_atom->haveOrientation() ){ |
650 | < | |
651 | < | dAtom = new DirectionalAtom(index); |
652 | < | simnfo->n_oriented++; |
653 | < | the_atoms[index] = dAtom; |
654 | < | |
655 | < | ux = current_atom->getOrntX(); |
656 | < | uy = current_atom->getOrntY(); |
657 | < | uz = current_atom->getOrntZ(); |
658 | < | |
659 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
660 | < | |
661 | < | u = sqrt( uSqr ); |
662 | < | ux = ux / u; |
663 | < | uy = uy / u; |
664 | < | uz = uz / u; |
665 | < | |
666 | < | dAtom->setSUx( ux ); |
667 | < | dAtom->setSUy( uy ); |
668 | < | dAtom->setSUz( uz ); |
669 | < | } |
670 | < | else{ |
671 | < | the_atoms[index] = new GeneralAtom(index); |
672 | < | } |
673 | < | the_atoms[index]->setType( current_atom->getType() ); |
674 | < | the_atoms[index]->setIndex( index ); |
675 | < | |
676 | < | // increment the index and repeat; |
677 | < | index++; |
678 | < | } |
679 | < | |
680 | < | molEnd = index -1; |
681 | < | the_molecules[lMolIndex].setNMembers( nMemb ); |
682 | < | the_molecules[lMolIndex].setStartAtom( molStart ); |
683 | < | the_molecules[lMolIndex].setEndAtom( molEnd ); |
684 | < | the_molecules[lMolIndex].setStampID( i ); |
685 | < | lMolIndex++; |
839 | > | |
840 | > | // init the atoms |
841 | ||
842 | < | #ifdef IS_MPI |
843 | < | } |
844 | < | #endif //is_mpi |
845 | < | |
846 | < | molIndex++; |
692 | < | } |
693 | < | } |
694 | < | |
695 | < | #ifdef IS_MPI |
696 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
842 | > | double ux, uy, uz, u, uSqr; |
843 | > | |
844 | > | atomOffset = 0; |
845 | > | excludeOffset = 0; |
846 | > | for(i=0; i<simnfo->n_mol; i++){ |
847 | ||
848 | < | delete[] globalIndex; |
848 | > | stampID = the_molecules[i].getStampID(); |
849 | ||
850 | < | mpiSim->mpiRefresh(); |
851 | < | #endif //IS_MPI |
852 | < | |
853 | < | the_ff->initializeAtoms(); |
854 | < | } |
850 | > | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
851 | > | info.nBonds = comp_stamps[stampID]->getNBonds(); |
852 | > | info.nBends = comp_stamps[stampID]->getNBends(); |
853 | > | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
854 | > | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
855 | ||
856 | < | void SimSetup::makeBonds( void ){ |
857 | < | |
858 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
859 | < | bond_pair* the_bonds; |
860 | < | BondStamp* current_bond; |
856 | > | info.myAtoms = &the_atoms[atomOffset]; |
857 | > | info.myExcludes = &the_excludes[excludeOffset]; |
858 | > | info.myBonds = new Bond*[info.nBonds]; |
859 | > | info.myBends = new Bend*[info.nBends]; |
860 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
861 | ||
862 | < | the_bonds = new bond_pair[tot_bonds]; |
863 | < | index = 0; |
864 | < | offset = 0; |
865 | < | molIndex = 0; |
866 | < | |
867 | < | for( i=0; i<n_components; i++ ){ |
868 | < | |
869 | < | for( j=0; j<components_nmol[i]; j++ ){ |
870 | < | |
871 | < | #ifdef IS_MPI |
722 | < | if( mpiSim->getMyMolStart() <= molIndex && |
723 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
724 | < | #endif // is_mpi |
862 | > | theBonds = new bond_pair[info.nBonds]; |
863 | > | theBends = new bend_set[info.nBends]; |
864 | > | theTorsions = new torsion_set[info.nTorsions]; |
865 | > | |
866 | > | // make the Atoms |
867 | > | |
868 | > | for(j=0; j<info.nAtoms; j++){ |
869 | > | |
870 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
871 | > | if( currentAtom->haveOrientation() ){ |
872 | ||
873 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
874 | < | |
875 | < | current_bond = comp_stamps[i]->getBond( k ); |
729 | < | the_bonds[index].a = current_bond->getA() + offset; |
730 | < | the_bonds[index].b = current_bond->getB() + offset; |
731 | < | |
732 | < | exI = the_bonds[index].a; |
733 | < | exJ = the_bonds[index].b; |
734 | < | |
735 | < | // exclude_I must always be the smaller of the pair |
736 | < | if( exI > exJ ){ |
737 | < | tempEx = exI; |
738 | < | exI = exJ; |
739 | < | exJ = tempEx; |
740 | < | } |
741 | < | |
742 | < | |
743 | < | #ifdef IS_MPI |
744 | < | |
745 | < | the_excludes[index*2] = |
746 | < | the_atoms[exI]->getGlobalIndex() + 1; |
747 | < | the_excludes[index*2 + 1] = |
748 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
749 | < | |
750 | < | #else // isn't MPI |
751 | < | |
752 | < | the_excludes[index*2] = exI + 1; |
753 | < | the_excludes[index*2 + 1] = exJ + 1; |
754 | < | // fortran index from 1 (hence the +1 in the indexing) |
755 | < | #endif //is_mpi |
756 | < | |
757 | < | // increment the index and repeat; |
758 | < | index++; |
759 | < | } |
760 | < | offset += comp_stamps[i]->getNAtoms(); |
873 | > | dAtom = new DirectionalAtom(j + atomOffset); |
874 | > | simnfo->n_oriented++; |
875 | > | info.myAtoms[j] = dAtom; |
876 | ||
877 | < | #ifdef IS_MPI |
877 | > | ux = currentAtom->getOrntX(); |
878 | > | uy = currentAtom->getOrntY(); |
879 | > | uz = currentAtom->getOrntZ(); |
880 | > | |
881 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
882 | > | |
883 | > | u = sqrt( uSqr ); |
884 | > | ux = ux / u; |
885 | > | uy = uy / u; |
886 | > | uz = uz / u; |
887 | > | |
888 | > | dAtom->setSUx( ux ); |
889 | > | dAtom->setSUy( uy ); |
890 | > | dAtom->setSUz( uz ); |
891 | } | |
892 | < | #endif //is_mpi |
892 | > | else{ |
893 | > | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
894 | > | } |
895 | > | info.myAtoms[j]->setType( currentAtom->getType() ); |
896 | > | |
897 | > | #ifdef IS_MPI |
898 | ||
899 | < | molIndex++; |
900 | < | } |
901 | < | } |
899 | > | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
900 | > | |
901 | > | #endif // is_mpi |
902 | > | } |
903 | > | |
904 | > | // make the bonds |
905 | > | for(j=0; j<info.nBonds; j++){ |
906 | > | |
907 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
908 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
909 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
910 | ||
911 | < | the_ff->initializeBonds( the_bonds ); |
912 | < | } |
911 | > | exI = theBonds[j].a; |
912 | > | exJ = theBonds[j].b; |
913 | ||
914 | < | void SimSetup::makeBends( void ){ |
915 | < | |
916 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
917 | < | bend_set* the_bends; |
918 | < | BendStamp* current_bend; |
919 | < | LinkedAssign* extras; |
779 | < | LinkedAssign* current_extra; |
780 | < | |
781 | < | |
782 | < | the_bends = new bend_set[tot_bends]; |
783 | < | index = 0; |
784 | < | offset = 0; |
785 | < | molIndex = 0; |
786 | < | for( i=0; i<n_components; i++ ){ |
787 | < | |
788 | < | for( j=0; j<components_nmol[i]; j++ ){ |
789 | < | |
914 | > | // exclude_I must always be the smaller of the pair |
915 | > | if( exI > exJ ){ |
916 | > | tempEx = exI; |
917 | > | exI = exJ; |
918 | > | exJ = tempEx; |
919 | > | } |
920 | #ifdef IS_MPI | |
921 | < | if( mpiSim->getMyMolStart() <= molIndex && |
922 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
923 | < | #endif // is_mpi |
921 | > | tempEx = exI; |
922 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
923 | > | tempEx = exJ; |
924 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
925 | > | |
926 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
927 | > | #else // isn't MPI |
928 | ||
929 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
929 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
930 | > | #endif //is_mpi |
931 | > | } |
932 | > | excludeOffset += info.nBonds; |
933 | > | |
934 | > | //make the bends |
935 | > | for(j=0; j<info.nBends; j++){ |
936 | > | |
937 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
938 | > | theBends[j].a = currentBend->getA() + atomOffset; |
939 | > | theBends[j].b = currentBend->getB() + atomOffset; |
940 | > | theBends[j].c = currentBend->getC() + atomOffset; |
941 | ||
942 | < | current_bend = comp_stamps[i]->getBend( k ); |
798 | < | the_bends[index].a = current_bend->getA() + offset; |
799 | < | the_bends[index].b = current_bend->getB() + offset; |
800 | < | the_bends[index].c = current_bend->getC() + offset; |
801 | < | |
802 | < | if( current_bend->haveExtras() ){ |
942 | > | if( currentBend->haveExtras() ){ |
943 | ||
944 | < | extras = current_bend->getExtras(); |
945 | < | current_extra = extras; |
944 | > | extras = currentBend->getExtras(); |
945 | > | current_extra = extras; |
946 | ||
947 | < | while( current_extra != NULL ){ |
948 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
947 | > | while( current_extra != NULL ){ |
948 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
949 | ||
950 | < | switch( current_extra->getType() ){ |
950 | > | switch( current_extra->getType() ){ |
951 | > | |
952 | > | case 0: |
953 | > | theBends[j].ghost = |
954 | > | current_extra->getInt() + atomOffset; |
955 | > | theBends[j].isGhost = 1; |
956 | > | break; |
957 | ||
958 | < | case 0: |
959 | < | the_bends[index].ghost = |
960 | < | current_extra->getInt() + offset; |
961 | < | the_bends[index].isGhost = 1; |
962 | < | break; |
817 | < | |
818 | < | case 1: |
819 | < | the_bends[index].ghost = |
820 | < | (int)current_extra->getDouble() + offset; |
821 | < | the_bends[index].isGhost = 1; |
822 | < | break; |
823 | < | |
824 | < | default: |
825 | < | sprintf( painCave.errMsg, |
826 | < | "SimSetup Error: ghostVectorSource was neiter a " |
827 | < | "double nor an int.\n" |
828 | < | "-->Bend[%d] in %s\n", |
829 | < | k, comp_stamps[i]->getID() ); |
830 | < | painCave.isFatal = 1; |
831 | < | simError(); |
832 | < | } |
833 | < | } |
958 | > | case 1: |
959 | > | theBends[j].ghost = |
960 | > | (int)current_extra->getDouble() + atomOffset; |
961 | > | theBends[j].isGhost = 1; |
962 | > | break; |
963 | ||
964 | < | else{ |
965 | < | |
966 | < | sprintf( painCave.errMsg, |
967 | < | "SimSetup Error: unhandled bend assignment:\n" |
968 | < | " -->%s in Bend[%d] in %s\n", |
969 | < | current_extra->getlhs(), |
970 | < | k, comp_stamps[i]->getID() ); |
971 | < | painCave.isFatal = 1; |
843 | < | simError(); |
844 | < | } |
845 | < | |
846 | < | current_extra = current_extra->getNext(); |
964 | > | default: |
965 | > | sprintf( painCave.errMsg, |
966 | > | "SimSetup Error: ghostVectorSource was neither a " |
967 | > | "double nor an int.\n" |
968 | > | "-->Bend[%d] in %s\n", |
969 | > | j, comp_stamps[stampID]->getID() ); |
970 | > | painCave.isFatal = 1; |
971 | > | simError(); |
972 | } | |
973 | } | |
974 | ||
850 | – | if( !the_bends[index].isGhost ){ |
851 | – | |
852 | – | exI = the_bends[index].a; |
853 | – | exJ = the_bends[index].c; |
854 | – | } |
975 | else{ | |
976 | ||
977 | < | exI = the_bends[index].a; |
978 | < | exJ = the_bends[index].b; |
977 | > | sprintf( painCave.errMsg, |
978 | > | "SimSetup Error: unhandled bend assignment:\n" |
979 | > | " -->%s in Bend[%d] in %s\n", |
980 | > | current_extra->getlhs(), |
981 | > | j, comp_stamps[stampID]->getID() ); |
982 | > | painCave.isFatal = 1; |
983 | > | simError(); |
984 | } | |
985 | ||
986 | < | // exclude_I must always be the smaller of the pair |
862 | < | if( exI > exJ ){ |
863 | < | tempEx = exI; |
864 | < | exI = exJ; |
865 | < | exJ = tempEx; |
866 | < | } |
867 | < | |
868 | < | |
869 | < | #ifdef IS_MPI |
870 | < | |
871 | < | the_excludes[(index + tot_bonds)*2] = |
872 | < | the_atoms[exI]->getGlobalIndex() + 1; |
873 | < | the_excludes[(index + tot_bonds)*2 + 1] = |
874 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
875 | < | |
876 | < | #else // isn't MPI |
877 | < | |
878 | < | the_excludes[(index + tot_bonds)*2] = exI + 1; |
879 | < | the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
880 | < | // fortran index from 1 (hence the +1 in the indexing) |
881 | < | #endif //is_mpi |
882 | < | |
883 | < | |
884 | < | // increment the index and repeat; |
885 | < | index++; |
986 | > | current_extra = current_extra->getNext(); |
987 | } | |
988 | < | offset += comp_stamps[i]->getNAtoms(); |
988 | > | } |
989 | > | |
990 | > | if( !theBends[j].isGhost ){ |
991 | > | |
992 | > | exI = theBends[j].a; |
993 | > | exJ = theBends[j].c; |
994 | > | } |
995 | > | else{ |
996 | ||
997 | < | #ifdef IS_MPI |
997 | > | exI = theBends[j].a; |
998 | > | exJ = theBends[j].b; |
999 | } | |
1000 | < | #endif //is_mpi |
1000 | > | |
1001 | > | // exclude_I must always be the smaller of the pair |
1002 | > | if( exI > exJ ){ |
1003 | > | tempEx = exI; |
1004 | > | exI = exJ; |
1005 | > | exJ = tempEx; |
1006 | > | } |
1007 | > | #ifdef IS_MPI |
1008 | > | tempEx = exI; |
1009 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1010 | > | tempEx = exJ; |
1011 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1012 | > | |
1013 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1014 | > | #else // isn't MPI |
1015 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1016 | > | #endif //is_mpi |
1017 | > | } |
1018 | > | excludeOffset += info.nBends; |
1019 | ||
1020 | < | molIndex++; |
1020 | > | for(j=0; j<info.nTorsions; j++){ |
1021 | > | |
1022 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1023 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1024 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1025 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1026 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1027 | > | |
1028 | > | exI = theTorsions[j].a; |
1029 | > | exJ = theTorsions[j].d; |
1030 | > | |
1031 | > | // exclude_I must always be the smaller of the pair |
1032 | > | if( exI > exJ ){ |
1033 | > | tempEx = exI; |
1034 | > | exI = exJ; |
1035 | > | exJ = tempEx; |
1036 | > | } |
1037 | > | #ifdef IS_MPI |
1038 | > | tempEx = exI; |
1039 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1040 | > | tempEx = exJ; |
1041 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1042 | > | |
1043 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1044 | > | #else // isn't MPI |
1045 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1046 | > | #endif //is_mpi |
1047 | } | |
1048 | < | } |
1048 | > | excludeOffset += info.nTorsions; |
1049 | ||
1050 | < | #ifdef IS_MPI |
1051 | < | sprintf( checkPointMsg, |
899 | < | "Successfully created the bends list.\n" ); |
900 | < | MPIcheckPoint(); |
901 | < | #endif // is_mpi |
902 | < | |
1050 | > | |
1051 | > | // send the arrays off to the forceField for init. |
1052 | ||
1053 | < | the_ff->initializeBends( the_bends ); |
1054 | < | } |
1053 | > | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1054 | > | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1055 | > | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1056 | > | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1057 | ||
907 | – | void SimSetup::makeTorsions( void ){ |
1058 | ||
1059 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
910 | < | torsion_set* the_torsions; |
911 | < | TorsionStamp* current_torsion; |
1059 | > | the_molecules[i].initialize( info ); |
1060 | ||
913 | – | the_torsions = new torsion_set[tot_torsions]; |
914 | – | index = 0; |
915 | – | offset = 0; |
916 | – | molIndex = 0; |
917 | – | for( i=0; i<n_components; i++ ){ |
1061 | ||
1062 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1062 | > | atomOffset += info.nAtoms; |
1063 | > | delete[] theBonds; |
1064 | > | delete[] theBends; |
1065 | > | delete[] theTorsions; |
1066 | > | } |
1067 | ||
1068 | #ifdef IS_MPI | |
1069 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1070 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1071 | < | #endif // is_mpi |
1069 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1070 | > | MPIcheckPoint(); |
1071 | > | #endif // is_mpi |
1072 | ||
1073 | < | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1073 | > | // clean up the forcefield |
1074 | > | the_ff->calcRcut(); |
1075 | > | the_ff->cleanMe(); |
1076 | ||
928 | – | current_torsion = comp_stamps[i]->getTorsion( k ); |
929 | – | the_torsions[index].a = current_torsion->getA() + offset; |
930 | – | the_torsions[index].b = current_torsion->getB() + offset; |
931 | – | the_torsions[index].c = current_torsion->getC() + offset; |
932 | – | the_torsions[index].d = current_torsion->getD() + offset; |
933 | – | |
934 | – | exI = the_torsions[index].a; |
935 | – | exJ = the_torsions[index].d; |
936 | – | |
937 | – | |
938 | – | // exclude_I must always be the smaller of the pair |
939 | – | if( exI > exJ ){ |
940 | – | tempEx = exI; |
941 | – | exI = exJ; |
942 | – | exJ = tempEx; |
943 | – | } |
944 | – | |
945 | – | |
946 | – | #ifdef IS_MPI |
947 | – | |
948 | – | the_excludes[(index + tot_bonds + tot_bends)*2] = |
949 | – | the_atoms[exI]->getGlobalIndex() + 1; |
950 | – | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
951 | – | the_atoms[exJ]->getGlobalIndex() + 1; |
952 | – | |
953 | – | #else // isn't MPI |
954 | – | |
955 | – | the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
956 | – | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
957 | – | // fortran indexes from 1 (hence the +1 in the indexing) |
958 | – | #endif //is_mpi |
959 | – | |
960 | – | |
961 | – | // increment the index and repeat; |
962 | – | index++; |
963 | – | } |
964 | – | offset += comp_stamps[i]->getNAtoms(); |
965 | – | |
966 | – | #ifdef IS_MPI |
967 | – | } |
968 | – | #endif //is_mpi |
969 | – | |
970 | – | molIndex++; |
971 | – | } |
972 | – | } |
973 | – | |
974 | – | the_ff->initializeTorsions( the_torsions ); |
1077 | } | |
1078 | ||
1079 | void SimSetup::initFromBass( void ){ |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |